COCOA                   Coordinate Covariation Analysis (COCOA)
aggregateLoadings       Use PCA loadings to score a region set
atf3_chr1               Atf3 binding regions.
brcaLoadings1           A matrix with loadings
brcaMCoord1             A data.frame object with coordinates for
                        cytosines from chr1 included in the PCA.
brcaMethylData1         A matrix with DNA methylation levels from
                        chromosome 1 for four patients.
brcaPCScores            A matrix with principal component scores for
                        PCs 1-4 for four breast cancer patients.
brcaPCScores657         A data.frame with principal component scores
                        for PCs 1-4 for 657 breast cancer patients as
                        well as a column with estrogen receptor status.
esr1_chr1               Estrogen receptor alpha binding regions.
gata3_chr1              Gata3 binding regions.
getLoadingProfile       Create a "meta-region" loading profile
nrf1_chr1               Nrf1 binding regions.
regionQuantileByPC      Visualize how individual regions are associated
                        with principal components
rsRankingIndex          Get indices for top scored region sets
rsScoreHeatmap          Heatmap of region set scores
rsScores                Example COCOA Results (made up)
runCOCOA                Do COCOA with many region sets
signalAlongPC           Visualize how genomic signal in a region set
                        changes along principal component axis
